3JQA

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-1,9-dihydro-6H-purine-6-thione (DX4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C7VPDB entry 2C7V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2932-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.997α = 90
b = 90.834β = 115.5
c = 82.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDPt coated mirrors in a Kirkpatrick-Baez (KB) geometry2006-05-21SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87300ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.957.6499.90.0570.0579.9378741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.90.320.322.13.311433

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2C7V1.957.6478702396099.870.1490.1470.189RANDOM23.802
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.22-0.541.63-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.73
r_dihedral_angle_4_deg16.781
r_dihedral_angle_3_deg13.448
r_dihedral_angle_1_deg5.566
r_scangle_it5.252
r_scbond_it4.05
r_mcangle_it2.828
r_mcbond_it2.418
r_angle_refined_deg1.342
r_angle_other_deg0.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.73
r_dihedral_angle_4_deg16.781
r_dihedral_angle_3_deg13.448
r_dihedral_angle_1_deg5.566
r_scangle_it5.252
r_scbond_it4.05
r_mcangle_it2.828
r_mcbond_it2.418
r_angle_refined_deg1.342
r_angle_other_deg0.937
r_mcbond_other0.638
r_symmetry_hbond_refined0.239
r_symmetry_vdw_other0.232
r_nbd_refined0.196
r_nbd_other0.182
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.124
r_nbtor_other0.084
r_chiral_restr0.073
r_xyhbond_nbd_other0.021
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7414
Nucleic Acid Atoms
Solvent Atoms638
Heterogen Atoms236

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOLREPphasing